proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 145 insertions, 0 deletions

diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
new file mode 100644
index 000000000000..ad017d9fc592
--- /dev/null
+++ b/sci-biology/shrimp/Manifest
@@ -0,0 +1,2 @@
+DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
+DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/shrimp/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
new file mode 100644
index 000000000000..771432f0bada
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="SHort Read Mapping Package"
+HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
+SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
+
+LICENSE="shrimp"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="custom-cflags"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="
+	!sci-biology/emboss
+	!sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+}
+
+src_prepare() {
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' Makefile || die
+}
+
+src_compile() {
+	append-flags -fopenmp
+	use custom-cflags || append-flags -O3 # per instructions in BUILDING
+	tc-export CXX
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	rm bin/README
+	dobin bin/*
+	insinto /usr/share/${PN}
+	doins -r utils
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING
+}
diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
new file mode 100644
index 000000000000..7f2033d9054a
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit flag-o-matic python-single-r1 toolchain-funcs
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="SHort Read Mapping Package"
+HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
+SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
+
+LICENSE="shrimp"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="custom-cflags +cpu_flags_x86_sse2"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="!sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}
+	${PYTHON_DEPS}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_pretend() {
+	use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
+}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+	python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e '1 a #include <stdint.h>' \
+		-i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed \
+		-e "s/LDFLAGS/LIBS/" \
+		-e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' \
+		-i Makefile || die
+
+	append-flags -fopenmp
+	if ! use custom-cflags; then
+		append-flags -O3
+		replace-flags -O* -O3
+	fi
+	tc-export CXX
+
+	cd utils || die
+	sed -e '/^#!/d' -i *py || die
+	sed -e '1i#!/usr/bin/python' -i *py || die
+}
+
+src_compile() {
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	local i
+	newdoc bin/README README.bin && rm bin/README
+	dobin bin/* utils/split-contigs utils/temp-sink
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
+
+	pushd utils > /dev/null
+
+	python_doscript *py
+
+	rm *.py *.o *.c split-contigs temp-sink || die
+	insinto /usr/share/${PN}
+	doins -r *
+}